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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of zebrafish to identify the molecular signatures integral to regenerating photoreceptors in the retina of the zebrafish

ABSTRACT: Investigating neuronal and photoreceptor regeneration in the retina of zebrafish has begun to yield insights into both the cellular and molecular means by which this lower vertebrate is able to repair its central nervous system. However, knowledge about the signaling molecules in the local microenvironment of a retinal injury and the transcriptional events they activate during neuronal death and regeneration is still lacking. To identify genes involved in photoreceptor regeneration, we combined light-induced photoreceptor lesions, laser-capture microdissection (LCM) of the outer nuclear layer (ONL) and analysis of gene expression to characterize transcriptional changes for cells in the ONL as photoreceptors die and are regenerated. Using this approach, we were able to characterize aspects of the molecular signature of injured and dying photoreceptors, cone photoreceptor progenitors and microglia within the ONL. We validated changes in gene expression and characterized the cellular expression for three novel, extracellular signaling molecules that we hypothesize are involved in regulating regenerative events in the retina. Experiment Overall Design: As a means to identify genes necessary for photoreceptor regeneration, we evaluated transcriptional changes for cells in the outer nuclear layer (ONL) as photoreceptors die and are regenerated. To accomplish this, we combined light-induced photoreceptor lesions, laser-capture microdissection (LCM) of the ONL and analysis of gene expression using oligonucleotide arrays.

ORGANISM(S): Danio rerio

SUBMITTER: Peter Hitchcock

PROVIDER: E-GEOD-13068 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identification of the molecular signatures integral to regenerating photoreceptors in the retina of the zebrafish

Project description:Investigating neuronal and photoreceptor regeneration in the retina of zebrafish has begun to yield insights into both the cellular and molecular means by which this lower vertebrate is able to repair its central nervous system. However, knowledge about the signaling molecules in the local microenvironment of a retinal injury and the transcriptional events they activate during neuronal death and regeneration is still lacking. To identify genes involved in photoreceptor regeneration, we combined light-induced photoreceptor lesions, laser-capture microdissection (LCM) of the outer nuclear layer (ONL) and analysis of gene expression to characterize transcriptional changes for cells in the ONL as photoreceptors die and are regenerated. Using this approach, we were able to characterize aspects of the molecular signature of injured and dying photoreceptors, cone photoreceptor progenitors and microglia within the ONL. We validated changes in gene expression and characterized the cellular expression for three novel, extracellular signaling molecules that we hypothesize are involved in regulating regenerative events in the retina.

2008-10-08 | GSE13068 | GEO

Transcription profiling of zebrafish retinal development and photoreceptor regeneration to investigate the roles of midkine-a and midkine-b

Project description:In the retina of adult teleosts, stem cells are sustained in two specialized niches: the ciliary marginal zone (CMZ) and the microenvironment surrounding adult MÃ¼ller glia. Recently, MÃ¼ller glia were identified as the regenerative stem cells in the teleost retina. Secreted signaling molecules that regulate neuronal regeneration in the retina are largely unknown. In a microarray screen to discover such factors, we identified midkine-b (mdkb). Midkine is a highly conserved heparin-binding growth factor with numerous biological functions. The zebrafish genome encodes two distinct midkine genes: mdka and mdkb. Here, we describe the cellular expression of mdka and mdkb during retinal development and the initial, proliferative phase of photoreceptor regeneration. The results show that in the embryonic and larval retina mdka and mdkb are expressed in stem cells, retinal progenitors and neurons in distinct patterns that suggest different functions for the two molecules. Following the selective death of photoreceptors in the adult, mdka and mdkb are co-expressed in horizontal cells and proliferating MÃ¼ller glia and their neurogenic progeny. These data reveal that Mdka and Mdkb are signaling factors present in the retinal stem cell niches in both embryonic and mature retinas, and that their cellular expression is actively modulated during retinal development and regeneration. Experiment Overall Design: As a means to identify genes necessary for photoreceptor regeneration, we evaluated transcriptional in the retina of the zebrafish as photoreceptors are regenerated. Albino zebrafish were dark adapted, then half were exposed to bright constant light and half were returned to normal lighting. After 72hrs of light exposure, retinal RNA was isolated and analysis of gene expression was performed using Affymetriz zebrafish gene arrays.

2009-01-13 | E-GEOD-13999 | biostudies-arrayexpress

Gene profiling of Müller glia during early stages of zebrafish photoreceptor regeneration

2009-02-04 | GSE14495 | GEO

Gene profiling of MÃ¼ller glia during early stages of zebrafish photoreceptor regeneration

Project description:Photoreceptor damage in adult mammals results in permanent cell loss and glial scarring in the retina. In contrast, adult zebrafish can regenerate photoreceptors following injury. By using a stable transgenic line in which GFP is driven by the cis-regulatory sequences of a glial specific marker gfap, Tg(gfap:GFP)mi2002, previous studies showed that MÃ¼ller glia, the radial glial cells in the retina, proliferate after photoreceptor loss and give rise to neuronal progenitors that eventually differentiate into regenerated photoreceptors. To identify the molecular mechanisms that initiate this regenerative response, MÃ¼ller glia were isolated from Tg(gfap:GFP)mi2002 fish during the early stages of regeneration after light lesion and gene expression profiles were generated by microarray analyses. Keywords: time course Retinas were dissected from Tg(gfap:GFP)mi2002 zebrafish at 8, 16, 24, 36 hour post-lesion (hpl) and non-light-treated controls (0 hpl) and were dissociated by enzymatic digestion. GFP+ MÃ¼ller glia were isolated by fluorescence-activated cell sorting (FACS) for RNA extraction and hybridization on Affymetrix microarrays. Independent hybridization of three biological replicates were performed for each time point.

2009-02-04 | E-GEOD-14495 | biostudies-arrayexpress

Transplanted human cones incorporate and function in a murine cone degeneration model

Project description:Once human photoreceptors die, they do not regenerate, thus photoreceptor transplantation has emerged as a potential treatment approach for blinding diseases. Improvements in transplant organization, donor cell maturation and synaptic connectivity to the host will be critical in advancing this technology to clinical practice. Unlike the unstructured grafts of prior cell suspension transplantations into end-stage degeneration models, we describe extensive incorporation of iPSC retinal organoid-derived human photoreceptors into mice with cone dysfunction. This incorporative phenotype was validated in both cone-only as well as pan-photoreceptor transplantations. Rather than forming a glial barrier, Müller cells extended throughout the graft, even forming a series of adherens junctions between mouse and human cells, reminiscent of an OLM. Donor-host interaction appeared to promote polarisation as well as development of morphological features critical for light detection, namely formation of inner and well stacked outer segments oriented towards the RPE. Putative synapse formation and graft function was evident both at a structural and electrophysiological level. Overall, these results show that human photoreceptors interact readily with a partially degenerated retina. Moreover, incorporation into the host retina appears to be beneficial to graft maturation, polarisation and function.

2022-06-01 | GSE201219 | GEO

Protective gene expression changes elicited by an inherited defect in photoreceptor structure.

Project description:To investigate pathogenic mechanisms in such instances, we have characterized rod photoreceptor and retinal gene expression changes in response to a defined insult to photoreceptor structure, using the retinal degeneration slow (rds) mouse model. Global gene expression profiling was performed on flow-sorted rds and wild-type rod photoreceptors immediately prior and subsequent to times at which OSs are normally elaborated. Dysregulated genes were identified via microarray hybridization, and selected candidates were validated using quantitative PCR analyses. We identified a single key gene, Egr1, that was dysregulated in a sustained fashion in rds rod photoreceptors and in the retina. Egr1 upregulation was associated with microglial activation and migration, into the outer retina at times subsequent to the major peak of photoreceptor cell death. Interestingly, this response was accompanied by neurotrophic factor upregulation. We hypothesize that activation of Egr1 and neurotrophic factors represents a protective immune mechanism, contributing to the characteristically slow retinal degeneration of the rds mouse model. We had two conditions WT and Rds-KO at 4 different time points: postnatal (P) 6, P9, P14 and P21.

2011-12-31 | E-GEOD-33134 | biostudies-arrayexpress

Protective gene expression changes elicited by an inherited defect in photoreceptor structure.

2011-12-31 | GSE33134 | GEO

Simultaneous absolute quantification of multiple proteins from the photoreceptor outer segment

Project description:This data set provides most accurate absolute quantification of outer segment proteins of rod photoreceptors of retina.

2022-12-12 | MSV000090885 | MassIVE

Single cell RNA-seq of CRX+ cells obtained at day 90 of retinal organoid differentiation

Project description:Death of photoreceptors and/or Retinal Pigment Epithelium (RPE) cells is a common cause of age related and inherited retinal dystrophies, thus their replenishment from renewable stem cell sources is a well sought therapeutic goal. Human pluripotent stem cells provide a useful cell source in view of their limitless self-renewal capacity and potential to differentiate into all key retinal cell types either in isolation or as part of three dimensional retinal organoids. Photoreceptor precursors have been isolated from differentiating human pluripotent stem cells either through application of cell surface markers or fluorescent reporter approaches and shown to share a transcriptional profile akin to foetal photoreceptors. In this study we investigated the transcriptional profile of CRX+ photoreceptor precursors derived from human embryonic stem cells (hESC) using single cell RNA sequencing and their engraftment capacity in an animal model of retinitis pigmentosa (C3H/rd1). Single cell RNA seq analysis revealed the presence of dominant cell cluster which displayed the hallmarks of early cone photoreceptor expression. When transplanted subretinally into the C3H/rd1 mice, the Crx positive cells settled next to the inner nuclear layer of host retina, matured into cone photoreceptors and made connections with the inner neurones of the host retina. Cellular transfer between the host retina and donor photoreceptors was investigated and shown to be minimal. Together our data provide valuable molecular insights into the transcriptional profile of human pluripotent stem cells derived CRX+ photoreceptor precursors and indicate their usefulness as a source of transplantable cone photoreceptors.

2019-04-01 | GSE112507 | GEO

Single-cell RNASeq analysis of human retinal organoids generated from hiPSC derived of a healthy donor patient

Project description:Results: Our histologic studies indicated that human retinal organoids (HROs) at day 200 of differentiation in this system are postmitotic and thus completed retinogenesis. Further, HRO contain all major retinal cell types in a laminated structure. Notably, HROs are cone photoreceptor-rich, show a 1:1:1 ratio of Müller glia, rod and cone photoreceptor. Immunostaining and ultrastructural studies showed that photoreceptors neurons mature, including photoreceptor inner and nascent outer segment formation. Our transcriptome analysis at the single cell level supports these findings. Further, comparison with published datasets (Voigt et al. 2019 [PMID: 31075224]) indicate that the genotype of cone photoreceptors in this HRO system correlates more strongly with the foveal cones of the human primary retina than peripheral cones. Müller glia show a trend towards human fovea whereas rod photoreceptors were found to be nearly similar. Conclusions: Single cell transcriptome analysis of HROs support and extend our findings at the histological level, indicating that HROs are cone photoreceptor-rich, and provide some characteristics of the human macula.

2022-09-01 | GSE174215 | GEO

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